.>>> * where do the dragons lurk .>>> .>> .>> webs of interconnected dynamically loaded libraries, identical versions of .>> R compiled with different BLAS/LAPACK options, etc. Go with the VM if you .>> really, truly, want this level of exact reproducibility. .> .> Sounds like the best bet -- maybe tools like vagrant might be useful here: .> .> http://www.vagrantup.com .> .> ... or maybe they're overkill? .> .> Haven't really checked it out myself too much, my impression is that .> these tools (vagrant, chef, puppet) are built to handle such cases. .> .> I'd imagine you'd probably need a location where you can grab the .> precise (versioned) packages for the things you are specifying, but . .Right...and this is a bit tricky, because we don't keep old versions .around in our BioC software repositories. They are available through .Subversion but with the sometimes additional overhead of setting up .build-time dependencies.
So, even if I wanted to go where dragons lurked, it would not be possible to cobble a version of biocLite that installed specific versions of software. Thus, I might rather consider an approach that at 'publish' time tarzips up a copy of the R package dependencies based on a config file defined from sessionInfo and caches it in the project directory. Then when/if the project is revisited (and found to produce differnt results under current R enviRonment), I can "simply" install an old R (oops, I guess I'd have to build it), and then un-tarzip the dependencies into the projects own R/Library which I would put on .libpaths. Or, or? (My virtual machine advocating colleagues are snickering now, I am sure......) Thanks for all your thoughts and advices.... --Malcolm . . .> ... .> .> -steve .> .> -- .> Steve Lianoglou .> Graduate Student: Computational Systems Biology .> | Memorial Sloan-Kettering Cancer Center .> | Weill Medical College of Cornell University .> Contact Info: http://cbio.mskcc.org/~lianos/contact .> .> ______________________________________________ .> R-devel@r-project.org mailing list .> https://stat.ethz.ch/mailman/listinfo/r-devel . ._______________________________________________ .Bioconductor mailing list .bioconduc...@r-project.org .https://stat.ethz.ch/mailman/listinfo/bioconductor .Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel